I did a full flush on my automatic transmission (06 V6 TRD Sport 2wd without towing package) today [45.1k miles]. I haven't seen any detailed DIY write up's on the process so here it goes (feel free to make sticky):

Overall it's very easy to do and not much more complicated than the standard ~3qt drain/fill. The process if you have the tow package is essentially the same, except your ATF cooling lines will be going to a small oil cooler vs going to the radiator. If you have a 4x4, the transmissions will look different than my pictures, but this may still help to guide you through the process.

Outside of having access to a flush machine, this is the next best thing – and free except fluid costs. A very small amount of original fluid does get mixed in, but it’s negligible. Without dropping the pan and attaching a special machine to the actual ATF pump, this works just as well as a standard flush machine. There is a metal screen (not a true filter) in the pan, but from everything posted prior, it’s not necessary to drop the pan and clean it this early – 100k miles or longer is fine.

Step 1: Loosen the fill plug (24mm - WS is stamped in the middle of it) on passenger side of transmission near the drive shaft, you can remove it or leave it in finger tight for now. The rubber o-ring can be reused here - take care not to damage it.

Step 2: Remove the drain plug (14mm) on the bottom of the transmission pan and be prepared to catch any fluid that comes out w/ your graduated bucket. Allow all fluid to come out, if your fluid is cold you should get about 3 quarts. You can rock the truck once it stops draining and get quite a bit more out, but this isn't necessary. Once the fluid has stopped draining, replace the 14mm plug w/ the new crush washer and tighten with torque wrench to 21 ft.*lb.

At this point you've drained about 3 qts, but take note of the precise amount you get.

Step 3: Remove the fill plug you loosened earlier - it's time to add an equal amount of new fluid that was removed from the drain plug. Route your oil pump hose into the fill hole and secure it. Pump in the proper amount. I added 3 qts. Once finished, remove the pump hose from the fill plug, you can leave the fill plug bolt out.

Step 4: Remove your skid plate if you have one. There are 4 bolts (12mm socket) securing it. This makes access for the next step substantially easier and will save you time.

Step 5: Locate the two ATF cooler lines on the passenger side of the transmission. You will see two lines close together running towards the front of the truck. The top line is the oil cooler outlet tube (fluid returns to the transmission in this line) and the bottom line is the oil cooler inlet tube (oil is pumped out of the transmission to the radiator or tow pkg cooler). You want the outlet tube (red) - trace this line the front of the truck to the point where the metal piping ends and the rubber hose is connected with a tube clamp. You’ll see 2 metal lines at the front of the truck just under the radiator and behind the frame. The top/forward most line is your return/outlet line. It eventually ends/connects to the bottom of your radiator or to your cooler. Disconnect the passenger side rubber hose (where red arrow is). The driver's side goes to the radiator(don't disconnect). Only a few drops came out when I disconnected it, so don't expect it to pour out and make a mess.

Loosen and slide this clamp down to free the connection between the hose and the piping. I needed to use pliers to *carefully* pull the hose off as it was stuck on there pretty good). Attach the 3/8 clear tubing to the metal pipe at the connection you just removed. You may need stretch the tubing out some on the end to get it on the metal pipe easier. once firmly attached, you can route the clear tube into your bucket (or use a clear jug with quart marks lined off - I opted to use this so I could see it filling easier).

Step 6: With the tube routed into your bucket, you're ready to start the engine and allow the fluid to pump out into the bucket. It pumps out at about 1 qt every 7 seconds. I did this by myself, but had enough time to start the engine, get out and watch it fill. Do NOT rev the engine, just let it idle. I turned the engine off once ~2.5 qts had pumped out. Be sure not to allow more than 2-3 quarts to come out, you don't want the internal pump to run dry. You can also shift from Park through all the gears if you wish, though I'm not sure if it makes a difference. I did this once for the heck of it.

At this point you've flushed out over half the old fluid (~3 qts from the drain pan + another ~2.5 qts from cooler/rad lines). This will be your original fluid and should give you an idea of how dirty it is.

Step 7: Time to add more new fluid - reconnect your oil pumper to the fill hole and add in approximately what you removed in the previous step. Once the new fluid has been added, remove the pump hose again from the fill hole. Dump out the old fluid in your bucket/jug into a waste container or the empty qt. containers. It's time to repeat step 6.

You will do these two steps several times to your liking. I would recommend repeating these steps until you've added at least 9 qts (not including the original 3 from the pan [total 12]) - although you'll notice by the time you've done step 6 twice, the fluid coming out is considerably cleaner and much redder.

You could probably get away with only adding the original 3 qts and doing the steps above with 7-8 qts (total of 10-11 new qts) to save some $$ on fluid. I ended up using 14 qts total, and the last 2 qts that came out almost looked like new fluid...so a little bit of a waste and probably overkill w/ this much.

Be sure to save at least 1 quart of new fluid in case you need to add more during the check level process.

Step 8: Once you've flushed ~12 quarts or the amount of your satisfaction, remove the 3/8 clear tubing from the ATF cooler line. A few drops will come out of the metal end, but not much, so don't worry about it gushing out. Reconnect the original rubber oil cooler outlet line to the metal piping going back to the transmission and put the tube clamp back in place. Assure that the line is snug and firmly attached. Clean up any ATF that may have spilled.

Step 9: You might want to add about 1/3 qt extra when you're all finished so that you don't have to do the fluid check level more than once - just let the extra drain out to the right level. Replace the fill plug bolt to hand tight - you'll torque it down later, or if you're forgetful you can do it now (29 ft.*lb).

Step 10: At this point you should have approximately the correct amount of fluid in the AT and everything is reconnected. It's time to perform the fluid level check to ensure that the right amount of fluid is in the transmission. I will briefly go over this as a great write up has already been done by ForTech (http://www.tacomaworld.com/forum/2nd-gen-tacomas/63851-how-drain-refill-automatic-transmission.html ). Do NOT use an IR thermometer - the pan reading won't be anywhere close to the internal temperature.

Cliffs notes version, but I highly suggest reading ForTech's post:

Make sure you're parked on level ground,
Start truck, shift through all gears several times to get new fluid moved all around.
Using a small wire, jump pins 4 and 13 on the ODBII port.
Start the truck, you should see a lot of your dash lights flashing.
From park, put truck in neutral for 2-3 seconds
Shift down to drive for ~1 second, enough for it to barely engage the gear then go back to neutral then back to drive after ~1 second. (repeat 3 times, total of 6 shifts).
Once back in neutral after 6th shift, you should see AT Temp in red light up for 2 seconds on the Tach face plate.
Shift back to park, you should see the AT temp light again for 2 seconds then go off. If you don't see this, you've messed up and need to do it again.
Let the truck idle until the AT temp light stays on. It's close when it starts flickering. It may take up to 20 minutes of idling to get to temp, especially in colder environments.

Step 11: With the AT Temp light on and the truck still idling, remove the check plug(5mm hex). Be mindful of the Y-pipe / exhaust as it's hot and you will burn yourself if more than lightly touched. Also have your catch bucket ready. Hopefully you've added a little more than what's needed and fluid will come out. Allow fluid to drain until it's a light/thin trickle. Add your new crush washer to the bolt and replace the bolt torquing to spec (15 ft.*lb). Turn the engine the off.

Step 12: If you had a good bit of fluid come out and are now at the proper level, torque down the refill plug(24mm / 29 ft.*lb) if you did not do so in step 9. If you did not add enough fluid - ie nothing came out - replace the check bolt, turn off the engine and then add 1/3 to 1/2 qt more new fluid into the fill plug. Go through the steps in Step 10 to the get the AT Temp sense mode back on and check the fluid again as described in step 11.

Step 13: Replace your skid plate if you removed it from step 4.
Step 14: Double check all your connections and bolts - Clean up any spilled fluid on truck.

That's it.

A few comparative pictures:
Original oil(left) / Brand new(right) [color is probably no indicator of usable life]

After 12 fresh quarts were flushed through (left)/ Brand new (right) [12qt sample was only slightly darker, but not much].

I will be sending a sample I took from the drain pan when it was hot to Blackstone to see what condition the oil was in after 45k miles. Should be a week or so and I'll append the results to affirm whether or not this early of a flush really needs to be done or not. Regardless - early/preventative maintenance is worth it to me.

Well the service guide recommends 60k for severe (towing, city driving, etc) and 100k miles standard (as a lifetime fluid ). The dealerships will say it's good for 100k miles and pretty much tell you to leave if you go in before that. I don't trust it for 100k miles, and when it's out of warranty at 60k, it's no skin off their back if it fails. Rumor has it Toyota just reduced it to 60k miles no matter what though.

I have a 2.7L Five lug 2x4. I do have a dip stick. I was wondering how closely this will be to what i need to do to flush my ATF. I have the Type iv fluid thats needed. But cant find how many qts i should expect to use.

So should I follow these instructions to a T. Or is their better instructions to follow.

Nope, this is for the sealed trans. on the 4.0L autos (no dipstick). I'm not sure what the specs are on the 2.7s, but you could use this as a baseline guide to fully flush your system if you want.

There should be similar cooler lines and the process would essentially be the same. I looked at my service cd, but didn't see any specs for the 2.7 on how much fluid the system takes, etc. Since you have a dipstick you could easily check levels. It needs to be done at 70 to 80 °C (158 to 176 °F) for the HOT reading. You may also have to fill it through that dipstick check line.

If you replace what you remove w/ the correct ATF type and your dipstick shows the right level, I think the rest should be fairly easy. Good luck, sorry I can't help more w/ the 2.7.